Unicellular Eukaryotes As Models in Cell and Molecular Biology
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Unicellular Eukaryotes as Models in Cell and Molecular Biology: Critical Appraisal of Their Past and Future Value Martin Simon*, Helmut Plattner†,1 *Molecular Cellular Dynamics, Centre of Human and Molecular Biology, Saarland University, Saarbru¨cken, Germany †Faculty of Biology, University of Konstanz, Konstanz, Germany 1Corresponding author: e-mail address: [email protected] Contents 1. Introduction 142 2. What is Special About Unicellular Models 143 2.1 Unicellular models 144 2.2 Unicellular models: Examples, pitfals, and perspectives 148 3. Unicellular Models for Organelle Biogenesis 151 3.1 Biogenesis of mitochondria in yeast 152 3.2 Biogenesis of secretory organelles, cilia, and flagella 152 3.3 Phagocytotic pathway 153 3.4 Qualifying for model system by precise timing 155 3.5 Free-living forms as models for pathogenic forms 157 4. Models for Epigenetic Phenomena 158 4.1 Epigenetic phenomena from molecules to ultrastructure 161 4.2 Models for RNA-mediated epigenetic phenomena 163 4.3 Excision of IESs during macronuclear development: scnRNA model 170 4.4 Maternal RNA controlling DNA copy number 172 4.5 Maternal RNA matrices providing template for DNA unscrambling in Oxytricha 172 4.6 Impact of epigenetic studies with unicellular models 173 5. Exploring Potential of New Model Systems 175 5.1 Human diseases as new models 175 5.2 Protozoan models: Once highly qualified Now disqualified? 178 5.3 Boon and bane of genome size: Small versus large 179 5.4 Birth and death of nuclei, rather than of cells 183 5.5 Special aspects 184 6. Epilogue 185 Acknowledgment 186 References 186 141 142 Abstract Unicellular eukaryotes have been appreciated as model systems for the analysis of cru- cial questions in cell and molecular biology. This includes Dictyostelium (chemotaxis, amoeboid movement, phagocytosis), Tetrahymena (telomere structure, telomerase function), Paramecium (variant surface antigens, exocytosis, phagocytosis cycle) or both ciliates (ciliary beat regulation, surface pattern formation), Chlamydomonas (flagellar biogenesis and beat), and yeast (S. cerevisiae) for innumerable aspects. Nowadays many problems may be tackled with “higher” eukaryotic/metazoan cells for which full geno- mic information as well as domain databases, etc., were available long before protozoa. Established molecular tools, commercial antibodies, and established pharmacology are additional advantages available for higher eukaryotic cells. Moreover, an increasing number of inherited genetic disturbances in humans have become elucidated and can serve as new models. Among lower eukaryotes, yeast will remain a standard model because of its peculiarities, including its reduced genome and availability in the haploid form. But do protists still have a future as models? This touches not only the basic under- standing of biology but also practical aspects of research, such as fund raising. As we try to scrutinize, due to specific advantages some protozoa should and will remain favor- able models for analyzing novel genes or specific aspects of cell structure and function. Outstanding examples are epigenetic phenomena a field of rising interest. 1. INTRODUCTION Eukaryotic cells are complex four dimensional systems, like a 4D puz zle, with molecular components varying in space and with time, for exam ple, after stimulation or during development. Furthermore, elements have to be routinely exchanged, for instance for repair work, as it occurs during molecular and organellar autophagy. All parts have to fit together at all times, not only in the individual organelles but in the cell as a whole and, in mul ticellular organisms, in the context of tissues. This makes it difficult to dissect individual aspects of cell structure, biogenesis, and function. Therefore, yeast and protists (protozoa and some algae), both endowed with some simple traits, have been appreciated as model systems over decades. In Section 2, we explore the possibility of using unicellular eukaryotes as models in the past and possibly also in the future. Mitochondria, Golgi apparatus, secretory organelles, cilia, and flagella look essentially the same throughout eukaryotes, from protists to mammals. Even plant cells follow essentially the same construction principle, disre garding the fact that, on the one hand, they harbor additional elements 143 (chloroplasts and their derivatives, glyoxysomes, etc.) and, on the other hand, they lack some components. Differences concern the lack of a centri ole, for instance in Angiosperms (flowering plants) and some Gymnosperms (Gnetales, Coniferae) (Hodges et al., 2012). Also some of the unicellular model organisms can live without a centriole (Bettencourt Dias, 2013; see Section 3), although centriole equivalents, the ciliary basal bodies, are present in unsurpassed numbers. This is an example of how unicellular organisms with particular traits can be favorable objects for the analysis of specific questions. In this context, the essential question we may ask a model system is which components are essential for centriole and which ones for basal body function. Taking advantage of specific traits of unicellular organisms has intensely facilitated the elaboration of new concepts in cell biology, as we will testify in this review. This view is not shared by all. For instance, Munro stated in a recent “highly accessed” article: “It is unlikely that the planet’s tax payers will be willing to pay for enough cell biologists to investigate every last intriguing invertebrate or bizarre bikont, and thus future work is likely to focus on particular key cell types, especially those found in tax payers themselves”(Munro, 2013). Does that mean the end of work with model cells, with any model? We here try to inves tigate the potential advantages and disadvantages of unicellular models with out talking up or down their advantages and their disadvantages. We are encouraged by a recent comment on “the genome’s rising stars,” where the perspectives of epigenetic research are appreciated (Maxmen, 2013): “Some experiments also call for experience with model systems...” As we outline in Section 4, epigenetics is one of the topics which promises a future par ticularly for protistan model systems. In Section 5, we try to give nonprotist models a fair chance. Finally, in Section 6, we try to reach an objective judg ment about the future of unicellular models. 2. WHAT IS SPECIAL ABOUT UNICELLULAR MODELS Nature provides a plethora of cells with special traits that appear aber rant when compared with “normal” cells, particularly when these are inte grated in a tissue such as liver. Consider, for instance, the example of the centriole in Section 1. However, deviations from what we consider “nor mal” from the mammalian point of view can not only fulfill special require ments in a “lower” eukaryote growing in the wild but may also offer to the 144 experimentalist a handle on specific problems which otherwise would be difficult to address. 2.1. Unicellular models To serve as a model, easy cultivation and established genomics are important prerequisites. In this section, we present lower eukaryotes preferably used as unicellular models, together with their systematic/evolutionary positions, and the type of problems for which they were or are still considered as models. 2.1.1 Dictyostelium (Amoebozoa, Mycetozoa) Dictyostelium (Amoebozoa, Mycetozoa) has served as a model for many aspects (Mu¨ller Taubenberger et al., 2013) including amoeboid movement and phagocytosis (Cosson and Soldati, 2008) as well as for cell adhesion (Annesley and Fisher, 2009; Bagorda and Parent, 2008; Harloff et al., 1989). Note that cell adhesion molecules were detected in Dictyostelium (Beug et al., 1973; Mu¨ller and Gerisch, 1978). They are of particular impor tance for this organism whose amoeba stage is capable of developmentally controlled cell aggregation (King et al., 2003; Williams et al., 2005). Haploid Dictyostelium cells greatly facilitate genetics studies. 2.1.2 Paramecium and Tetrahymena (Alveolata, Ciliata) Paramecium and Tetrahymena (Alveolata, Ciliata), mainly P. tetraurelia and T. thermophila, have served as models for the function (Sleigh, 1969) and bio genesis (Smith et al., 2005) of cilia. In ciliates, metachronal waves of ciliary beat (Fig. 3.1) are easy to study. Because of the surface mucus layer on mam malian ciliated epithelia it was impossible to analyze their metachronal beat which in ciliates is clearly imposed by hydrodynamic coupling. Only recently has this phenomenon been formally described on a more general basis (Elgeti and Gompper, 2013). The regular construction of the cortex of Tetrahymena and Paramecium (Fig. 3.2) was helpful in analyzing pattern formation, with epigenetic effects involved (Aufderheide et al., 1980; Frankel, 1973). This regularity also greatly facilitated the analysis of exocy tosis and endocytosis (Section 3.4). Study of phagocytosis under precisely timed conditions was another aspect (Allen and Fok, 2000). In Paramecium, synchronous exocytosis of a large number of dense core secretory organ elles, the trichocysts, can be achieved (Plattner et al., 1984), because a cell contains up to 1000 trichocysts ready for immediate release upon 145 Figure 3.1 Scanning electron micrograph of the surface of a Paramecium cell. Cilia are arranged in waves due to metachronal beat activity. Already early on, the great number of cilia and easy accessibility of Paramecium to electrophysiology have made this cell an invaluable model. Magnification 1100Â. Unpublished